Nearly 40 percent of MTA employees making more than $150,000 a year are rank-and-file workers, a new analysis of the agency’s payroll shows.

That’s due to outdated work rules that allow unionized employees to rake in astounding amounts of overtime and bonus pay — perks that MTA brass have tried to squash as they face a $400 million deficit for 2010.

The money-sucking problem is especially bad on the LIRR and Metro-North.

According to numbers crunched by The Empire Center, 65 conductors on the commuter railroads averaged $86,837 in overtime alone. That’s on top of their base salaries, which averaged about $80,000.

Also, 53 Bridges and Tunnels sergeants and lieutenants averaged $94,962 in OT. Their average base pay is $82,594.

The list of those topping $150,000 goes on to include railroad engineers, MTA police officers and LIRR work-gang foremen.

One rule gives LIRR workers an extra day’s pay for switching between a diesel and an electric train in the middle of a shift.

Another rule mandates that five bus drivers be added to the Q53 Rockaway Beach route every weekend in July and August — rain or shine.

In bad weather, when no one is at the beach, those drivers still get paid — to sit in a work room.

“We are in the process of overhauling every aspect of our business, including the elimination of approximately 3,000 positions this year,” the MTA said in a statement.

Overtime is particularly in the crosshairs.

“One key part is a focus on the work rules, pension padding and management oversight that leads to some of the unnecessary overtime highlighted in today’s report,” it added.

The Empire Center report noted that there was a 2.4 percent overall increase in salary payouts at the MTA in 2009, even though the number of employees dropped.